Mercurial > repos > mingchen0919 > rmarkdown_collection_builder

annotate collection_list.Rmd @ 13:ff1cb127967e draft

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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 6df7b8ef3a603f7792ed5815ff324ede8a7b2b0b-dirty
author mingchen0919
date Mon, 25 Sep 2017 16:19:14 -0400
parents f5b1f7d4db53
children b4adc08beae7
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87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
parents:
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1 ---
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
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2 title: 'Collection builder (collection type: list)'
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
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3 output:
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
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4 html_document:
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
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5 number_sections: true
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
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6 toc: true
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
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7 theme: cosmo
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
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8 highlight: tango
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
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9 ---
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
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87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
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11 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
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12 knitr::opts_chunk$set(
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
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13 echo = ECHO
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
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14 )
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
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15 ```
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
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9c2059916485 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 6df7b8ef3a603f7792ed5815ff324ede8a7b2b0b-dirty
mingchen0919
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17 # Command line arguments
9c2059916485 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 6df7b8ef3a603f7792ed5815ff324ede8a7b2b0b-dirty
mingchen0919
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ff1cb127967e planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 6df7b8ef3a603f7792ed5815ff324ede8a7b2b0b-dirty
mingchen0919
parents: 12
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19 ```{r 'command line arguments'}
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87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
parents:
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20 str(opt)
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
parents:
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21 ```
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f85a6bcf940e planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571-dirty
mingchen0919
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f85a6bcf940e planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571-dirty
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ff1cb127967e planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 6df7b8ef3a603f7792ed5815ff324ede8a7b2b0b-dirty
mingchen0919
parents: 12
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24 ```{r 'rename files'}
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f5b1f7d4db53 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 6df7b8ef3a603f7792ed5815ff324ede8a7b2b0b-dirty
mingchen0919
parents: 11
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25 # create directory
f5b1f7d4db53 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 6df7b8ef3a603f7792ed5815ff324ede8a7b2b0b-dirty
mingchen0919
parents: 11
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26 dir.create('./files_directory')
f5b1f7d4db53 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 6df7b8ef3a603f7792ed5815ff324ede8a7b2b0b-dirty
mingchen0919
parents: 11
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27 # get full paths of original files
f5b1f7d4db53 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 6df7b8ef3a603f7792ed5815ff324ede8a7b2b0b-dirty
mingchen0919
parents: 11
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28 from_files = strsplit("FILE_LIST", ',')[[1]]
f5b1f7d4db53 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 6df7b8ef3a603f7792ed5815ff324ede8a7b2b0b-dirty
mingchen0919
parents: 11
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29 # copy files to the created directory.
f5b1f7d4db53 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 6df7b8ef3a603f7792ed5815ff324ede8a7b2b0b-dirty
mingchen0919
parents: 11
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30 file.copy(from_files, './files_directory')
f5b1f7d4db53 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 6df7b8ef3a603f7792ed5815ff324ede8a7b2b0b-dirty
mingchen0919
parents: 11
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31 # get original file names
f5b1f7d4db53 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 6df7b8ef3a603f7792ed5815ff324ede8a7b2b0b-dirty
mingchen0919
parents: 11
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32 original_files = list.files('./files_directory')
f5b1f7d4db53 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 6df7b8ef3a603f7792ed5815ff324ede8a7b2b0b-dirty
mingchen0919
parents: 11
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33 # create new files names from original file names
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ff1cb127967e planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 6df7b8ef3a603f7792ed5815ff324ede8a7b2b0b-dirty
mingchen0919
parents: 12
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34 new_files = gsub('\\.dat', '\\.FORMAT', original_files)
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f5b1f7d4db53 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 6df7b8ef3a603f7792ed5815ff324ede8a7b2b0b-dirty
mingchen0919
parents: 11
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35 # rename files
f5b1f7d4db53 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 6df7b8ef3a603f7792ed5815ff324ede8a7b2b0b-dirty
mingchen0919
parents: 11
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36 file.copy(paste0('./files_directory/', original_files),
f5b1f7d4db53 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 6df7b8ef3a603f7792ed5815ff324ede8a7b2b0b-dirty
mingchen0919
parents: 11
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37 paste0('./files_directory/', new_files))
f5b1f7d4db53 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 6df7b8ef3a603f7792ed5815ff324ede8a7b2b0b-dirty
mingchen0919
parents: 11
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38 ```
f5b1f7d4db53 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 6df7b8ef3a603f7792ed5815ff324ede8a7b2b0b-dirty
mingchen0919
parents: 11
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39
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ff1cb127967e planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 6df7b8ef3a603f7792ed5815ff324ede8a7b2b0b-dirty
mingchen0919
parents: 12
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40 # End